Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A14 F1 I2 R1 774 49.2 2112398 96.9% 2046913 118.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,765,794 (C)7→8 intergenic (‑18/‑124) yfjM ← / → rnlA CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, RNase LS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,765,7871.C98.2% 194.0 / ‑3.4 57intergenic (‑11/‑131)yfjM/rnlACP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, RNase LS
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base C (20/36);  total (21/36)
Fisher's exact test for biased strand distribution p-value = 3.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.31e-01

GGCTCTCTGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAAT  >  NC_000913/2765650‑2765919
                                                                                                                                          |                                                                                                                                     
ggCTCTCTGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTg                                                                                                                                        >  2:271592/1‑138 (MQ=255)
ggCTCTCTGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTg                                                                                                                                        <  1:271592/138‑1 (MQ=255)
   tctctGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTTTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑cc‑cc                                                                                                                                  <  1:831152/139‑1 (MQ=255)
    ctctGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑cc‑ccc                                                                                                                                 <  1:297176/139‑1 (MQ=255)
    ctctGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑cc‑ccc                                                                                                                                 <  2:426108/139‑1 (MQ=255)
     tctGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑cc‑cccc                                                                                                                                <  1:370249/139‑1 (MQ=255)
              tCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGAc                                                                                                                        >  2:629862/1‑139 (MQ=255)
                  tttCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATc                                                                                                                    <  1:194436/139‑1 (MQ=255)
                  tttCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATc                                                                                                                    <  1:715794/139‑1 (MQ=255)
                  tttCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATc                                                                                                                    <  1:868433/139‑1 (MQ=255)
                  tttCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATc                                                                                                                    <  2:865616/139‑1 (MQ=255)
                  tttCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATc                                                                                                                    <  1:477368/139‑1 (MQ=255)
                  tttCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATc                                                                                                                    <  2:276932/139‑1 (MQ=255)
                        cGTAGAATTTTCTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGATTGCCC‑CCCCCGGTAGACGATCCTGccc                                                                                                              <  1:682767/139‑1 (MQ=255)
                          tAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCta                                                                                                            >  2:228948/1‑139 (MQ=255)
                          tAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCta                                                                                                            >  1:876866/1‑139 (MQ=255)
                                   ttCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAg                                                                                                   <  2:819507/139‑1 (MQ=255)
                                   ttCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAg                                                                                                   <  1:361520/139‑1 (MQ=255)
                                   ttCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAg                                                                                                   <  2:1034378/139‑1 (MQ=255)
                                   ttCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAg                                                                                                   <  1:169046/139‑1 (MQ=255)
                                   ttCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAg                                                                                                   <  2:464814/139‑1 (MQ=255)
                                                          aCTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATc                                                                                                                    <  1:106414/99‑1 (MQ=255)
                                                          aCTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATc                                                                                                                    >  2:106414/1‑99 (MQ=255)
                                                              aGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                       <  2:646074/139‑1 (MQ=255)
                                                              aGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                       <  1:851589/139‑1 (MQ=255)
                                                              aGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                       >  2:851589/1‑139 (MQ=255)
                                                              aGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                       <  1:228948/139‑1 (MQ=255)
                                                              aGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                       >  1:825746/1‑139 (MQ=255)
                                                              aGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                       <  2:178972/139‑1 (MQ=255)
                                                              aGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                       <  2:825746/139‑1 (MQ=255)
                                                                  tCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTg                                                                                                                 <  1:833167/94‑1 (MQ=255)
                                                                  tCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTg                                                                                                                 >  2:833167/1‑94 (MQ=255)
                                                                   cGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                  <  2:423748/139‑1 (MQ=255)
                                                                   cGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CCTCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAAt                                                                  >  1:539603/1‑139 (MQ=255)
                                                                          ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATaca                                                           >  2:676945/1‑139 (MQ=255)
                                                                          ctgctTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATaca                                                           >  2:410264/1‑139 (MQ=255)
                                                                                  tGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg                                                   <  1:319082/139‑1 (MQ=255)
                                                                                  tGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg                                                   <  1:676945/139‑1 (MQ=255)
                                                                                     gaTCAGGAAGAGGTTTCCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAgggggg                                                <  2:833538/139‑1 (MQ=255)
                                                                                         aGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                             >  1:543260/1‑122 (MQ=255)
                                                                                         aGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                             <  2:543260/122‑1 (MQ=255)
                                                                                                ggTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg                                                   >  1:493126/1‑125 (MQ=255)
                                                                                                ggTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAggg                                                   <  2:493126/125‑1 (MQ=255)
                                                                                                ggTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTag                                     >  1:662168/1‑139 (MQ=255)
                                                                                                ggTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTag                                     >  2:135248/1‑139 (MQ=255)
                                                                                                   tACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGt                                  <  2:662168/139‑1 (MQ=255)
                                                                                                     ccGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAg                                                                                                   <  2:200250/73‑1 (MQ=255)
                                                                                                     ccGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAg                                                                                                   >  1:200250/1‑73 (MQ=255)
                                                                                                          aCGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCa                           <  1:171966/139‑1 (MQ=255)
                                                                                                           cGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATc                                                                                                                    >  1:109802/1‑50 (MQ=255)
                                                                                                           cGATGGACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATc                                                                                                                    <  2:109802/50‑1 (MQ=255)
                                                                                                               ggACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                             >  2:553032/1‑100 (MQ=255)
                                                                                                               ggACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATa                                                             <  1:553032/100‑1 (MQ=255)
                                                                                                               ggACATCATCCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGt                      <  2:539603/139‑1 (MQ=255)
                                                                                                                      atcCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCATATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATg               <  2:876866/139‑1 (MQ=255)
                                                                                                                       tcCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAg                                                                                                   <  1:922191/55‑1 (MQ=255)
                                                                                                                       tcCCCCATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAg                                                                                                   >  2:922191/1‑55 (MQ=255)
                                                                                                                           ccATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGccc                                                                                                              >  2:696978/1‑40 (MQ=255)
                                                                                                                           ccATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGccc                                                                                                              <  1:696978/40‑1 (MQ=255)
                                                                                                                           ccATTTTGTGGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATc          <  2:330483/139‑1 (MQ=255)
                                                                                                                                  gtgGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                       <  1:935345/71‑1 (MQ=255)
                                                                                                                                  gtgGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCAGGTGGCTAAATTTAg                                                                       >  2:935345/1‑71 (MQ=255)
                                                                                                                                   tgGACTGCCC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTG‑CCCCTATTCCGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTCTTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAAt  >  2:170889/1‑139 (MQ=255)
                                                                                                                                          |                                                                                                                                     
GGCTCTCTGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTG‑CC‑CCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGGGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAAT  >  NC_000913/2765650‑2765919

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A