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
A1 F21 I0 R1 476 35.3 2812105 96.7% 2719305 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,866,110 T→A 100% intergenic (‑20/+160) rpoS ← / ← nlpD RNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,866,1100TA100.0% 99.9 / NA 35intergenic (‑20/+160)rpoS/nlpDRNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (22/13);  total (22/13)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAAT  >  W3110S.gb/2866046‑2866160
                                                                |                                                  
cacacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTcta                                              >  1:48638/1‑71 (MQ=255)
  cacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact                                            <  1:1387945/71‑1 (MQ=255)
  cacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctac                                             >  1:731392/1‑70 (MQ=255)
            ggCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc                                                <  1:566133/57‑1 (MQ=255)
            ggCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtttt                                  >  1:2562881/1‑71 (MQ=255)
              cTCCCTGCGATAACAGTTGCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTc                                 >  1:195371/1‑70 (MQ=255)
              cTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCg                                >  1:1030753/1‑71 (MQ=255)
              cTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGACCTTTTCg                                >  1:638364/1‑71 (MQ=255)
                     cGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa                           <  1:802252/69‑1 (MQ=255)
                       aTAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa                          <  1:1100781/68‑1 (MQ=255)
                       aTAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAAcc                       >  1:260665/1‑71 (MQ=255)
                        tAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAtt                                                 >  1:1409210/1‑44 (MQ=255)
                         aaCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTcta                                              >  1:978540/1‑46 (MQ=255)
                         aaCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTcta                                              >  1:916152/1‑46 (MQ=255)
                         aaCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTcta                                              >  1:393966/1‑46 (MQ=255)
                         aaCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCt                      >  1:2169462/1‑70 (MQ=255)
                         aaCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCt                      >  1:2511447/1‑70 (MQ=255)
                             gTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACt                 <  1:12523/71‑1 (MQ=255)
                                ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAAtt                                                 >  1:1965457/1‑36 (MQ=255)
                                ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtttt                                  >  1:1441791/1‑51 (MQ=255)
                                ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCaa                   >  1:421908/1‑66 (MQ=255)
                                ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCaa                   >  1:425124/1‑66 (MQ=255)
                                 ctctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCaa                   >  1:1624739/1‑65 (MQ=255)
                                 ctctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGt             >  1:183697/1‑71 (MQ=255)
                                         ccAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca     <  1:296869/71‑1 (MQ=255)
                                          cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCaa    <  1:1300949/71‑1 (MQ=255)
                                          cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCaa    <  1:926628/71‑1 (MQ=255)
                                           aaaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCaa    >  1:525124/1‑70 (MQ=255)
                                            aaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa                          >  1:2262252/1‑47 (MQ=255)
                                             aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAAt  >  1:142988/1‑70 (MQ=255)
                                                gTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc                     <  1:597001/48‑1 (MQ=255)
                                                gTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc                     <  1:1238621/48‑1 (MQ=255)
                                                gTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc                     <  1:1123670/48‑1 (MQ=255)
                                                        tGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc                     <  1:1505122/40‑1 (MQ=255)
                                                        tGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc                     <  1:1336634/40‑1 (MQ=255)
                                                                |                                                  
CACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAAT  >  W3110S.gb/2866046‑2866160

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A