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
A8 F1 I1 R1 771 44.8 2153074 94.1% 2026042 109.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,712,518 (C)6→7 intergenic (+360/‑251) nth → / → dtpA DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,712,5121.C97.4% 128.4 / ‑3.2 38intergenic (+354/‑257)nth/dtpADNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (22/15);  total (22/16)
Fisher's exact test for biased strand distribution p-value = 4.21e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.50e-01

TCAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑A‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGACTT  >  NC_000913/1712377‑1712639
                                                                                                                                         |                                                                                                                               
tCAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACATACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAATCCATC‑A‑ccc                                                                                                                              >  2:759851/1‑139 (MQ=255)
 cAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑A‑cccc                                                                                                                             <  2:273590/139‑1 (MQ=255)
  aGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑A‑ccccc                                                                                                                            <  1:78289/139‑1 (MQ=255)
                                         gACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑A‑cc                                                                                                                               >  1:946569/1‑97 (MQ=255)
                                         gACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑A‑cc                                                                                                                               <  2:946569/97‑1 (MQ=255)
                                         gACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGCACTATCTCACTAGTGAAAACGCTAAATAGCAGAACATATCGCCGATAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGCAAAAATCTGCCGTTACGtttttt                                                                                      >  2:707663/1‑139 (MQ=255)
                                           ccTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATA‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGa                                                                                    >  2:1058150/1‑139 (MQ=255)
                                               cAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGaaaaa                                                                                >  2:627853/1‑139 (MQ=255)
                                                         cacTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTg                                                                      >  2:381336/1‑139 (MQ=255)
                                                            tGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGAt                                                                   >  2:398989/1‑139 (MQ=255)
                                                              gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGa                                                                    >  2:49053/1‑136 (MQ=255)
                                                              gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGa                                                                    <  1:49053/136‑1 (MQ=255)
                                                              gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATaa                                                                 >  1:1034095/1‑139 (MQ=255)
                                                                                    aTCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAAtt                                           >  1:940174/1‑139 (MQ=255)
                                                                                     tctcACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTc                                          >  2:907367/1‑139 (MQ=255)
                                                                                       tcACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTccc                                        <  2:940174/139‑1 (MQ=255)
                                                                                          cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGc                                     <  1:627853/139‑1 (MQ=255)
                                                                                          cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑A‑cc                                                                                                                               >  2:262545/1‑48 (MQ=255)
                                                                                          cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑A‑cc                                                                                                                               <  1:262545/48‑1 (MQ=255)
                                                                                           tAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc                                    <  1:907367/139‑1 (MQ=255)
                                                                                            aGTAGAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                   <  1:1026676/139‑1 (MQ=255)
                                                                                            aGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                   <  1:866/139‑1 (MQ=255)
                                                                                            aGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCGCTGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                   <  2:1034095/139‑1 (MQ=255)
                                                                                             gTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGc                                     <  1:278975/136‑1 (MQ=255)
                                                                                             gTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGc                                     >  2:278975/1‑136 (MQ=255)
                                                                                               aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                   <  2:323736/136‑1 (MQ=255)
                                                                                               aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                   >  1:204633/1‑136 (MQ=255)
                                                                                               aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                   >  1:323736/1‑136 (MQ=255)
                                                                                               aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                   <  2:204633/136‑1 (MQ=255)
                                                                                               aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAg                                >  1:990795/1‑139 (MQ=255)
                                                                                               aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAACCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCGCGCCTCAg                                >  1:638921/1‑139 (MQ=255)
                                                                                                 aaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGtt                              <  1:1058150/139‑1 (MQ=255)
                                                                                                   aCGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTtat                            >  1:423121/1‑139 (MQ=255)
                                                                                                    cGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTtata                           <  1:398989/139‑1 (MQ=255)
                                                                                                     gCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTcag                                                                                                                     >  1:595201/1‑48 (MQ=255)
                                                                                                     gCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTcag                                                                                                                     <  2:595201/48‑1 (MQ=39)
                                                                                                       tAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGaa                                                     <  1:800035/110‑1 (MQ=255)
                                                                                                       tAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGaa                                                     >  2:800035/1‑110 (MQ=255)
                                                                                                       tAAATAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGt                        >  1:245744/1‑139 (MQ=255)
                                                                                                        aaaTAGCAGAACATATCGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTa                       >  1:159810/1‑139 (MQ=255)
                                                                                                         aaTATCAGAACCTTTCCCCGTTAATCCATCTC‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGTTAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTaa                      <  2:245744/139‑1 (MQ=255)
                                                                                                                        cGCCGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAg       >  1:537005/1‑139 (MQ=255)
                                                                                                                           cGTTAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGAc    <  2:802177/139‑1 (MQ=255)
                                                                                                                             ttAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGACtt  >  2:197623/1‑139 (MQ=255)
                                                                                                                             ttAAGCCATC‑ACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGACtt  >  1:769976/1‑139 (MQ=255)
                                                                                                                                         |                                                                                                                               
TCAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATC‑A‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGACTT  >  NC_000913/1712377‑1712639

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A