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
A9 F110 I0 R1 50 71.1 1529928 95.4% 1459551 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,440,085 G→T 100% intergenic (‑45/‑891) cspA ← / → xpaC cold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,440,0850GT97.7% 159.7 / ‑5.4 55intergenic (‑45/‑891)cspA/xpaCcold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC
Reads supporting (aligned to +/- strand):  ref base G (0/1);  major base T (23/29);  minor base A (0/2);  total (23/32)
Fisher's exact test for biased strand distribution p-value = 5.02e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTA  >  CP000730/1439949‑1440221
                                                                                                                                        |                                                                                                                                        
gAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAACCCTCCAAGACTAAAATTCATTAAATCTGCTTATTCTCata                                                                                                                                      >  2:28176/1‑141 (MQ=255)
gAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCata                                                                                                                                      >  1:40459/1‑141 (MQ=255)
        tACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaa                                                                                                                              >  1:729842/1‑141 (MQ=255)
             aTACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATAc                                                                                                                         <  1:570030/141‑1 (MQ=255)
             aTACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATAc                                                                                                                         <  1:750504/141‑1 (MQ=255)
                     ttttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAAt                                                                                                                 >  1:442445/1‑141 (MQ=255)
                        tctcCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTc                                                                                                              <  2:758393/141‑1 (MQ=255)
                             ttCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCa                                                                                                         <  1:691219/141‑1 (MQ=255)
                             ttCAAACTCGATAAAGCCGAATCCTCTTTCAGCGTTAATCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGTCTATAATTCATTCAATATGCTTATTAAAAAAATAAAAAAAATACAGGCAAATTTCACTCa                                                                                                         <  2:516182/141‑1 (MQ=255)
                              tCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCaa                                                                                                        <  1:760825/141‑1 (MQ=255)
                              tCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAAATCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCaa                                                                                                        >  1:610521/1‑141 (MQ=255)
                              tCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAAATCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCaa                                                                                                        >  1:410295/1‑141 (MQ=255)
                                 ccTTCGAAAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGGCCCCTGTTACAAAATCTTACACCTCCAAAACTAAAATTCATTCAATATGCTTATTCTCATATTACAATAAATACATGCAGTTTTAACTCAAata                                                                                                     <  2:297711/140‑1 (MQ=255)
                                  cTTCGATAAAGCCGAATCCCTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAAGTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAatat                                                                                                    <  1:120336/141‑1 (MQ=255)
                                   ttCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATAtt                                                                                                   <  1:32257/141‑1 (MQ=255)
                                     cGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCt                                                                                                 >  1:85498/1‑141 (MQ=255)
                                      gacaaaGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTTTTTCCTAATAGGATAAATCCCAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAAAATTCtt                                                                                                >  2:92511/4‑141 (MQ=255)
                                      gATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt                                                                                                >  2:510630/1‑141 (MQ=255)
                                      gATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt                                                                                                <  2:359596/141‑1 (MQ=255)
                                      gATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt                                                                                                <  2:64011/141‑1 (MQ=255)
                                         aaaGCCGAATCTTTTTACATCGTTAAACCATTTAACTTTACCTTGTTTCACAATCTGAAACCTTCAAGACTAAAATTCATTCAATATGCTTATTCAAAAATAAAAAAAAATACATGCAAATTTCACTCAAATATTCTTTGc                                                                                             <  2:517316/141‑1 (MQ=255)
                                         aaaGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGc                                                                                             <  1:231154/141‑1 (MQ=255)
                                         aaaGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATGCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGc                                                                                             <  1:525220/141‑1 (MQ=255)
                                             ccGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAata                                                                                         <  2:697346/141‑1 (MQ=255)
                                               gAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTTCAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATg                                                                                       >  1:206618/1‑141 (MQ=255)
                                                  tCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCACTATGGaa                                                                                    <  1:472729/141‑1 (MQ=255)
                                                  tCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCGCCAAGACTAAAATTCATTCACTATGCTTATTCTCATATAACAAAAAATGCATTCAAATTTCATCAAAATGTTCTTTCCAATATGGaa                                                                                    >  1:661068/1‑141 (MQ=255)
                                                   ccTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaaa                                                                                   >  2:76031/1‑140 (MQ=255)
                                                       tttCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatc                                                                               >  1:26754/1‑141 (MQ=255)
                                                           aGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCt                                                                           <  2:390341/141‑1 (MQ=255)
                                                               ttAAACCATTTAACTGTACCTTTTTTCATAATCTGAAACCTCCAAGTCGAAAATTCACTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCtt                                                                       <  2:729842/141‑1 (MQ=255)
                                                                      aTTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGt                                                                <  2:425800/141‑1 (MQ=255)
                                                                                   ttGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGt                                                   >  1:468497/1‑141 (MQ=255)
                                                                                      tttCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTCTTATAGTGCAGttat                                                >  1:728131/1‑141 (MQ=255)
                                                                                      tttCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttat                                                <  1:232657/141‑1 (MQ=255)
                                                                                      tttCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttat                                                >  1:251373/1‑141 (MQ=255)
                                                                                               ttGAACCTTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAAtt                                       <  2:741826/140‑1 (MQ=255)
                                                                                                   aaCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaa                                   >  1:743540/1‑141 (MQ=255)
                                                                                                     ccTCCCAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaata                                 <  1:303462/141‑1 (MQ=255)
                                                                                                      cTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTGCACTCAAATATTCTTTGCAATATGGAATAATCCTCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaatac                                >  1:335067/1‑141 (MQ=255)
                                                                                                       tCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaataca                               <  2:62849/141‑1 (MQ=255)
                                                                                                       tCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaaaaaa                               <  2:255945/141‑5 (MQ=255)
                                                                                                         cAATACTAAAAGTCATTCAATATGCGTATTCTCATATTACAAAAAATACATGCAAATTACACTCAAATATTCTTTTCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaatacaat                             <  2:499646/141‑1 (MQ=255)
                                                                                                         cAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaatacaat                             <  1:138660/141‑1 (MQ=255)
                                                                                                            aaCTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACaataat                          <  1:738049/140‑1 (MQ=255)
                                                                                                             aCTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAataata                         <  2:588581/141‑1 (MQ=255)
                                                                                                             aCTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAataata                         <  1:282750/141‑1 (MQ=255)
                                                                                                             aCTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACGCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCATATATTACCAAATTGCAATACAataata                         >  1:464235/1‑141 (MQ=255)
                                                                                                                  atttcattcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaaaa                    <  1:698893/139‑1 (MQ=255)
                                                                                                                             tatGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAATTATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTaa         >  2:161966/1‑141 (MQ=255)
                                                                                                                             tatGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGTAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTaa         <  1:510630/141‑1 (MQ=255)
                                                                                                                             tatGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTaa         <  2:442445/141‑1 (MQ=255)
                                                                                                                              atGCTTATTCTCATATGACAACAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAAt        >  1:388889/1‑141 (MQ=255)
                                                                                                                                   tATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAatt   >  1:707459/1‑141 (MQ=255)
                                                                                                                                    aTTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAatta  >  1:327446/1‑141 (MQ=255)
                                                                                                                                        |                                                                                                                                        
GAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTA  >  CP000730/1439949‑1440221

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A