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
A22 F44 I0 R1 387 90.4 3244086 98.5% 3195424 139.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,333,003 C→T 7.8% pseudogene (1400/4605 nt) yfaS ← pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,333,0030CT 7.8% 157.3 / 4.3 51pseudogene (1400/4605 nt)yfaSpseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein
Reads supporting (aligned to +/- strand):  ref base C (21/26);  new base T (2/2);  total (23/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.05e-01

CGTTTCGCTGCCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGCTTGATGTAGTTTGCCACGCGAAAACTGCTGCTATAGACCTGATTGCGGTAAGCAAGACGTAACTCATAACCTC  >  NC_000913/2332858‑2333141
                                                                                                                                                 |                                                                                                                                          
cGTTTCGCTGCCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGc                                                                                                                                         <  1:123640/149‑1 (MQ=255)
      gCTGCCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTg                                                                                                                                       >  1:281551/1‑145 (MQ=255)
      gCTGCCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTg                                                                                                                                       <  2:281551/145‑1 (MQ=255)
          ccTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTc                                                                                                                               <  3:67916/149‑1 (MQ=255)
          ccTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTc                                                                                                                               <  3:660460/149‑1 (MQ=255)
              ccAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCa                                                                                                                           >  3:546506/1‑149 (MQ=255)
              ccAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCa                                                                                                                           >  1:560797/1‑149 (MQ=255)
                         gggAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGTCGCTGACCGCTTCGCCAGTTTTGAActc                                                                                                                >  1:27994/1‑149 (MQ=255)
                         gggAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGTCGCTGACCGCTTCGCCAGTTTTGAActc                                                                                                                >  1:58128/1‑149 (MQ=255)
                                gTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTg                                                                                                         <  4:305207/149‑1 (MQ=255)
                                   cGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCg                                                                                                      >  2:549009/1‑149 (MQ=255)
                                          aCGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTa                                                                                               >  2:787456/1‑149 (MQ=255)
                                            gCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTaaa                                                                                             >  3:799942/1‑149 (MQ=255)
                                                aTCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCaa                                                                                         >  1:663998/1‑149 (MQ=255)
                                                 tCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAAt                                                                                        <  1:544825/149‑1 (MQ=255)
                                                 tCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAAt                                                                                        <  1:549009/149‑1 (MQ=255)
                                                  cGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAAtc                                                                                       <  4:320675/149‑1 (MQ=255)
                                                    ttACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAAtctc                                                                                     <  1:787456/149‑1 (MQ=255)
                                                     tACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAAtctct                                                                                    >  4:22972/1‑148 (MQ=255)
                                                        cGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGaaa                                                                                 <  4:799942/149‑1 (MQ=255)
                                                           ccATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGagag                                                                                                  <  1:80028/129‑1 (MQ=255)
                                                           ccATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGagag                                                                                                  >  2:80028/1‑129 (MQ=255)
                                                            cATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGTCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAAtgtg                                                                             <  2:58128/149‑1 (MQ=255)
                                                            cATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGTCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAAtgtg                                                                             <  2:27994/149‑1 (MQ=255)
                                                            cATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAAtgtg                                                                             <  1:72244/149‑1 (MQ=255)
                                                             aTTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTgg                                                                            >  3:199318/1‑149 (MQ=255)
                                                                 aTAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGCTTg                                                                        <  4:283689/149‑1 (MQ=255)
                                                                   aaTTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGCTTGAt                                                                      >  1:448655/1‑149 (MQ=255)
                                                                    aTTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGCTTGATg                                                                     >  1:770319/1‑149 (MQ=255)
                                                                      tGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGCTTGATGTa                                                                   <  1:696914/149‑1 (MQ=255)
                                                                                      ttAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGc                                                                                                                                         <  4:298729/63‑1 (MQ=255)
                                                                                      ttAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGc                                                                                                                                         >  3:298729/1‑63 (MQ=255)
                                                                                          cTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGCTTGATGTAGTTTGCCACGCGAAAActgc                                               >  2:201970/1‑149 (MQ=255)
                                                                                              aCGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGaa                                                                                  >  3:535945/1‑110 (MQ=255)
                                                                                              aCGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGACAGCTAAACCAATCTCGaa                                                                                  <  4:535945/110‑1 (MQ=255)
                                                                                                 cgGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGCTTGATGTAGTTTGCCACGCGAAAACTGCTGCtata                                        <  4:359864/149‑1 (MQ=255)
                                                                                                      aTTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGATCTAAACCAATCTCGAAATGTGGCTTGATGTAGTTTGCCACGCGAAAACTGCTGCTATAGACCt                                   <  4:546506/149‑1 (MQ=255)
                                                                                                      aTTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGCTTGATGTAGTTTGCCACGCGAAAACTGCTGCTATAGACCt                                   <  2:560797/149‑1 (MQ=255)
                                                                                                         ttttACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGCTTGATGTAGTTTGCCACGCGAAAACTGCTGCTATAGACCTGAt                                >  1:215349/1‑149 (MQ=255)
                                                                                                            tACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGc                                                                           >  2:197051/1‑103 (MQ=255)
                                                                                                            tACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGc                                                                           <  1:197051/103‑1 (MQ=255)
                                                                                                              ccGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAAtgtg                                                                             <  4:106163/99‑1 (MQ=255)
                                                                                                              ccGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAAtgtg                                                                             >  3:106163/1‑99 (MQ=255)
                                                                                                                 gCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGCTTGATGTAGTTTGCCACGCGAAAACTGCTGCTATAGACCTGATTGCGGTaa                        <  2:215349/149‑1 (MQ=255)
                                                                                                                     gCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGCTTGATGTAGTTTGCCACGCGAAAACTGCTGCTATAGACCTGATTGCGGTAAGCaa                    >  3:427650/1‑149 (MQ=255)
                                                                                                                     gCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGCTTGATGTAGTTTGCCACGCGAAAACTGCTGCTATAGACCTGATTGCGGTAAGCaa                    <  4:427650/149‑1 (MQ=255)
                                                                                                                        aTCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGCTTGATGTAGTTTGCCACGCGAAAACTGCTGCTATAGACCTGATTGCGGTAAGCAAGAc                 <  3:22972/149‑1 (MQ=255)
                                                                                                                        aTCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGCTTGATGTAGTTTGCCACGCGAAAACTGCTGCTATAGACCTGATTGCGGTAAGCAAGAc                 >  1:61068/1‑149 (MQ=255)
                                                                                                                                   gcagttgcagttTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGCTTGATGTAGTTTGCCACGCGAAAACTGCTGCTATAGACCTGATTGCGGTAAGCAAGACGTAACTCATaa      <  1:208918/149‑1 (MQ=255)
                                                                                                                                      gttgcagttTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGCTTGATGTAGTTTGCCACGCGAAAACTGCTGCTATAGACCTGATTGCGGTAAGCAAGACGTAACTCATAACCt   >  3:800280/1‑149 (MQ=255)
                                                                                                                                       ttgcagttTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGCTTGATGTAGTTTGCCACGCGAAAACTGCTGCTATAGACCTGATTGCGGTAAGCAAGACGTAACTCATAACCTc  <  1:201970/149‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                          
CGTTTCGCTGCCTTCCAGCGACACGGGGAAACGTCCGGCATAACGCAAATCGTTACCGACCATTGATAATTGCTGAGCGCGCAAACTTAACTGCACGCGGGCATTTTTTACCGGCTCGCCATCCGGGTAGAGCAGTTGCAGTTTGCCGCTGACCGCTTCGCCAGTTTTGAACTCTTTTTTGGCGAGAGCTAAACCAATCTCGAAATGTGGCTTGATGTAGTTTGCCACGCGAAAACTGCTGCTATAGACCTGATTGCGGTAAGCAAGACGTAACTCATAACCTC  >  NC_000913/2332858‑2333141

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A