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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,583,611 A→G 37.5% N227N (AAT→AAC)  zipA ← cell division protein involved in Z ring assembly

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,583,6110AG37.5% 22.8 / 28.4 48N227N (AAT→AAC) zipAcell division protein involved in Z ring assembly
Reads supporting (aligned to +/- strand):  ref base A (14/16);  new base G (12/6);  total (26/22)
Fisher's exact test for biased strand distribution p-value = 2.37e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.05e-01

TTCGCCAGGCTGAATAACGCCGGGCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGCTGTTAAGAAGCAGTTCACCGTTTAGCTCGC  >  minE/1583552‑1583678
                                                           |                                                                   
ttCGCCAGGCTGAATAACGCCGGGCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATc                                                             >  1:1529589/1‑68 (MQ=255)
         cTGAATAACGCCGGGCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATGTTCATATCGCCAAAAATg                                                   <  1:1767562/69‑1 (MQ=255)
         cTGAATAACGCCGGGCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATGTTCATATCGCCAAAAATg                                                   <  1:2940449/69‑1 (MQ=255)
         cTGAATAACGCCGGGCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATGTTCATATCGCCAAAAATg                                                   <  1:588625/69‑1 (MQ=255)
         cTGAATAACGCCGGGCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATGTTCATATCGCCAAAAATg                                                   <  1:3243703/69‑1 (MQ=255)
          tGAATAACGCCGGTCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATGTTCATATCGCCAAAAATg                                                   <  1:669618/68‑1 (MQ=255)
                aCGCCGGGCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCg                                            >  1:2515927/1‑69 (MQ=255)
                aCGCCGGGCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCg                                            >  1:1577642/1‑69 (MQ=255)
                aCGCCGGGCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCg                                            >  1:492515/1‑69 (MQ=255)
                aCGCCGGGCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCg                                            >  1:557448/1‑69 (MQ=255)
                aCGCCGGGCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCg                                            >  1:1028696/1‑69 (MQ=255)
                       gCCGCTGCCATCCGGGCTAAGATGACGATTGTAAATATTCATATCGCCAAAAATGAAGCCCGCttgttg                                     <  1:874507/69‑1 (MQ=255)
                       gCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCttgttg                                     <  1:3403378/69‑1 (MQ=255)
                       gCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCttgttg                                     <  1:317948/69‑1 (MQ=255)
                       gCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCttgttg                                     <  1:502417/69‑1 (MQ=255)
                       gCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCttgttg                                     <  1:2932753/69‑1 (MQ=255)
                       gCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCttgttg                                     <  1:2881254/69‑1 (MQ=255)
                       gCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCttgttg                                     <  1:2790211/69‑1 (MQ=255)
                       gCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCttgttg                                     <  1:106613/69‑1 (MQ=255)
                       gCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCttgttg                                     <  1:1921345/69‑1 (MQ=255)
                       gCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCttgttg                                     <  1:1267681/69‑1 (MQ=255)
                       gCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCttgttg                                     <  1:1347869/69‑1 (MQ=255)
                       gCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCttgttg                                     <  1:1356792/69‑1 (MQ=255)
                        ccGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTAATATCGCCAAAAATGAAGCCCGCttgttg                                     <  1:435088/68‑1 (MQ=255)
                            tGCCATCCGGGCTAAGATGACGATGGTAAATGTTCATATCGCCAAAAATg                                                   <  1:1101560/50‑1 (MQ=255)
                             gCCATCCGGGCTAAGATGACGCTGGTAAATATTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGc                                >  1:1848709/1‑68 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATGTTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGCt                               >  1:3416815/1‑69 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATGTTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGCt                               >  1:1430450/1‑69 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATGTTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGCt                               >  1:3201964/1‑69 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATGTTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGCt                               >  1:1442941/1‑69 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATGTTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGCt                               >  1:3033935/1‑69 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATGTTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGCt                               >  1:1374417/1‑69 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATGTTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGCt                               >  1:604318/1‑69 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATGTTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGCt                               >  1:2560486/1‑69 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATGTTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGCt                               >  1:2375449/1‑69 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATGTTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGCt                               >  1:2293709/1‑69 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATGTTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGCt                               >  1:2284586/1‑69 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATGTTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGCt                               >  1:2156089/1‑69 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGc                                >  1:1369441/1‑68 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGc                                >  1:890560/1‑68 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGc                                >  1:425904/1‑68 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGc                                >  1:14240/1‑68 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGc                                >  1:1855128/1‑68 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGc                                >  1:2841748/1‑68 (MQ=255)
                             gCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGc                                >  1:2180994/1‑68 (MQ=255)
                                            aTGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGCTGTTAAGAAGCAGt                  <  1:1668142/67‑1 (MQ=255)
                                               aCGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGCTGTTAAGAAGCAg                   <  1:2988645/63‑1 (MQ=255)
                                                      tAAATATTCATATCGCCAAAAATGAAGCCCGCttgttg                                     <  1:2301162/38‑1 (MQ=255)
                                                          tatTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGCTGTTAAGAAGCAGTTCACCGTTTAGCTCGc  <  1:2829743/69‑1 (MQ=255)
                                                          tatTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGCTGTTAAGAAGCAGTTCACCGTTTAGCTCGc  <  1:1912047/69‑1 (MQ=255)
                                                           |                                                                   
TTCGCCAGGCTGAATAACGCCGGGCCGCTGCCATCCGGGCTAAGATGACGATGGTAAATATTCATATCGCCAAAAATGAAGCCCGCTTGTTGAATGCTGTTAAGAAGCAGTTCACCGTTTAGCTCGC  >  minE/1583552‑1583678

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