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
A11 F142 I1 R1 99 64.8 3148104 96.3% 3031624 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,853,312 T→C intergenic (‑324/‑241) ivbL ← / → tisB ilvB operon leader peptide/toxic membrane persister formation peptide, LexA‑regulated

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,853,3120TC98.3% 194.4 / ‑4.2 58intergenic (‑324/‑241)ivbL/tisBilvB operon leader peptide/toxic membrane persister formation peptide, LexA‑regulated
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (27/30);  total (27/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.88e-01

GCAGAACGCGCAATTTCGGCACGAATTTTGACGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTATACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTCCTGGCTGAAACGGGTGGTGCCG  >  NC_000913/3853215‑3853408
                                                                                                 |                                                                                                
gcAGAACGCGCAATTTCGGCACGAATTTTGACGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTacac                                                                                                <  2:962970/100‑1 (MQ=255)
  aGAACGCGCAATTTCGGCACGAATTTTGACGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAg                                                                                              <  1:560944/100‑1 (MQ=255)
   gAACGCGCAATTTCGGCACGAATTTTGACGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGt                                                                                             <  2:28901/100‑1 (MQ=255)
      cgcgCAATTTCGGCACGAATTTTGACGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGt                                                                                             <  2:29013/97‑1 (MQ=255)
       gcgcAATTTCGGCACGAATTTTGACGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAAc                                                                                         <  1:922639/100‑1 (MQ=255)
        ttccgatctggCACGAATTTTGACGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACt                                                                                        <  1:1154882/91‑1 (MQ=255)
        cgcAATTTCGGCACGAATTTTGACGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACt                                                                                        >  1:668311/1‑100 (MQ=255)
        cgcAATTTCGGCACGAATTTTGACGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACt                                                                                        <  2:429420/100‑1 (MQ=255)
              ttCGGCACGAATTTTTACTTATTTAGTGCATAGTTTAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCtata                                                                                  <  2:935164/100‑1 (MQ=255)
                cGGCACGAATTTTGACGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACATTAAACTTCTataat                                                                                >  1:1530073/1‑100 (MQ=255)
                 ggCACGAATTTTGACGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACtagatcggaa                                                                               >  2:1154875/1‑91 (MQ=255)
                 ggCACGAATTTTGACGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTataata                                                                               <  1:1047124/100‑1 (MQ=255)
                     cGAATTTTGACGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCAc                                                                           >  2:352542/1‑100 (MQ=255)
                     cGAATTTTGACGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCAc                                                                           <  2:794204/100‑1 (MQ=255)
                     cGAATTTTGACGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCAc                                                                           >  1:755883/1‑100 (MQ=255)
                            tGACGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGc                                                                    <  2:322743/100‑1 (MQ=255)
                            tGACGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGc                                                                    <  2:386775/100‑1 (MQ=255)
                            tGACGTATTTAGTACATAGTTGAGTATCGATCACAGTTGGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGc                                                                    >  2:968475/1‑100 (MQ=255)
                              aCGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCaa                                                                  >  1:8156/1‑100 (MQ=255)
                                   tttAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACCCAGTAAACTTCTATAATATCACTGTACGCAATgtgt                                                             >  1:191833/1‑100 (MQ=255)
                                   tttAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATgtgt                                                             <  2:668308/100‑1 (MQ=255)
                                    ttAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGtt                                                            >  2:10397/1‑100 (MQ=255)
                                      aGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTAt                                                          <  2:313741/100‑1 (MQ=255)
                                      aGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTAt                                                          <  2:77259/100‑1 (MQ=255)
                                         gCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGc                                                        >  2:40277/1‑99 (MQ=255)
                                         gCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCg                                                       >  2:1137514/1‑100 (MQ=255)
                                          cATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCgg                                                      <  1:325641/100‑1 (MQ=255)
                                            tAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCgggg                                                    >  2:230990/1‑100 (MQ=255)
                                             aGTTGAGTATCGATAACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCGCTGTACGCAATGTGTTATGCggggg                                                   <  2:897634/100‑1 (MQ=255)
                                              gTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGc                                                  >  2:1041112/1‑100 (MQ=255)
                                                tGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCg                                                <  2:332703/100‑1 (MQ=255)
                                                tGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCg                                                >  2:656122/1‑100 (MQ=255)
                                                 gAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGc                                               <  1:1215983/100‑1 (MQ=255)
                                                  aGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCa                                              <  2:316773/100‑1 (MQ=255)
                                                  aGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCa                                              <  1:1085901/100‑1 (MQ=255)
                                                  aGTATAGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCgaa                                              >  2:315936/1‑98 (MQ=255)
                                                       cGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGtt                                         <  1:10397/100‑1 (MQ=255)
                                                        gATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTa                                        >  2:112349/1‑100 (MQ=255)
                                                          tCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTAcc                                      <  2:773787/100‑1 (MQ=255)
                                                           cacaGTTTGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTAccc                                     <  1:612854/100‑1 (MQ=255)
                                                                 ttGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCa                               <  2:768306/100‑1 (MQ=255)
                                                                  tGCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCAc                              >  2:527165/1‑100 (MQ=255)
                                                                   gCGTTTTGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACt                             >  2:1211988/1‑100 (MQ=255)
                                                                       tttGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGt                         <  1:602589/100‑1 (MQ=255)
                                                                       tttGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGt                         <  1:902801/100‑1 (MQ=255)
                                                                         tGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTcc                       >  2:516133/1‑100 (MQ=255)
                                                                         tGTCCAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTcc                       >  2:1132531/1‑100 (MQ=255)
                                                                            ccAAATATTACTGTTTATTTATACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTCCTgg                    <  1:1129967/100‑1 (MQ=255)
                                                                             cAAATATTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTCCTGGc                   >  2:1554132/1‑100 (MQ=255)
                                                                             cAAATATTACTGTATATTTACACAGTCAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTACTGGc                   >  2:936563/1‑100 (MQ=255)
                                                                                  atTACTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTCCTGGCTGaaa              <  1:215403/100‑1 (MQ=255)
                                                                                     aCTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTCCTGGCTGAAACgg           >  1:1300181/1‑100 (MQ=255)
                                                                                     aCTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTCCTGGCTGAAACgg           >  2:907298/1‑100 (MQ=255)
                                                                                      cTGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTCCTGGCTGAAACggg          <  2:35335/100‑1 (MQ=255)
                                                                                       tGTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTCCTGGCTGAAACGggt         <  1:1379775/100‑1 (MQ=255)
                                                                                        gTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTCCTGGCTGAAACGggtg        <  2:3806/100‑1 (MQ=255)
                                                                                        gTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTCCTGGCTGAAACGggtg        >  2:116946/1‑100 (MQ=255)
                                                                                        gTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTCCTGGCTGAAACGggtg        >  1:1132281/1‑100 (MQ=255)
                                                                                        gTTTATTTACACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTCCTGGCTGAAACGggtg        >  1:1453754/1‑100 (MQ=255)
                                                                                            atttacACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTCCTGGCTGAAACGGGTGGTGc    <  1:1380456/100‑1 (MQ=255)
                                                                                             tttacACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTCCTGGCTGAAACGGGTGGTGcc   >  2:616255/1‑100 (MQ=255)
                                                                                             tttacACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTCCTGGCTGAAACGGGTGGTGcc   >  1:669157/1‑100 (MQ=255)
                                                                                              ttacACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTCCTGGCTGAAACGGGTGGTGCCg  >  2:1348362/1‑100 (MQ=255)
                                                                                                 |                                                                                                
GCAGAACGCGCAATTTCGGCACGAATTTTGACGTATTTAGTGCATAGTTGAGTATCGATCACAGTTTGCGTTTTGTCCAAATATTACTGTTTATTTATACAGTAAACTTCTATAATATCACTGTACGCAATGTGTTATGCGGGGGCCGCATCGTTACCCGGCGCACTAAGTCCTGGCTGAAACGGGTGGTGCCG  >  NC_000913/3853215‑3853408

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A