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 2,615,623 A→G 57.2% G56G (GGA→GGG)  yhhS → predicted transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,615,6230AG57.2% 13.2 / 33.9 49G56G (GGA→GGG) yhhSpredicted transporter
Reads supporting (aligned to +/- strand):  ref base A (9/12);  new base G (20/8);  total (29/20)
Fisher's exact test for biased strand distribution p-value = 7.71e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGCCGCTCGCTGTATTACCGGGCTATGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCATGCCGGACGT  >  minE/2615559‑2615680
                                                                |                                                         
tGCCGCTCGCTGTATTACCGGGCTATGTCCATGATGTAATGGGATTTAGTGCATTCTGGGCAGGGTTgg                                                       <  1:2917829/69‑1 (MQ=255)
tGCCGCTCGCTGTATTACCGGGCTATGTCCATGATGTAATGGGATTTAGTGCATTCTGGGCAGGGTTgg                                                       <  1:2804559/69‑1 (MQ=255)
tGCCGCTCGCTGTATTACCGGGCTATGTCCATGATGTAATGGGATTTAGTGCATTCTGGGCAGGGTTgg                                                       <  1:435322/69‑1 (MQ=255)
tGCCGCTCGCTGTATTACCGGGCTATGTCCATGATGTAATGGGATTTAGTGCATTCTGGGCAGGGTTgg                                                       <  1:1909190/69‑1 (MQ=255)
tGCCGCTCGCTGTATTACCGGGCTATGTCCATGATGTAATGGGATTTAGTGCATTCTGGGCAGGGTTgg                                                       <  1:1779177/69‑1 (MQ=255)
tGCCGCTCGCTGTATTACCGGGCTATGTCCATGATGTAATGGGATTTAGTGCATTCTGGGCAGGGTTgg                                                       <  1:3367554/69‑1 (MQ=255)
tGCCGCTCGCTGTATTACCGAGCTATGTCCATGATGTAATGGGATTTAGTGCATTCTGGGCAGGGTTgg                                                       <  1:2943659/69‑1 (MQ=255)
       cgctGTATTACCGGGCTATGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGGTTGGTTATCAg                                                <  1:1631420/69‑1 (MQ=255)
       cgctGTATTACCGGGCTATGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGATTGGTTATCAg                                                <  1:105014/69‑1 (MQ=255)
       cgctGTATTACCGGGCTATGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGATTGGATATCAg                                                <  1:437772/69‑1 (MQ=255)
           gTATTACCGGGCTATGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGAt                                                          >  1:1146617/1‑55 (MQ=255)
           gTATTACCGGGCTATGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGATTGGt                                                      >  1:1170594/1‑59 (MQ=255)
           gTATTACCGGGCTATGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGATTGGt                                                      >  1:2561282/1‑59 (MQ=255)
           gTATTACCGGGCTATGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGATTGGt                                                      >  1:3026414/1‑59 (MQ=255)
           gTATTACCGGGCTATGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGATTGGt                                                      >  1:1152475/1‑59 (MQ=255)
           gTATTACCGGGCTATGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGATTGGt                                                      >  1:3182961/1‑59 (MQ=255)
                aCCGGGCTATGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTGCAata                                       >  1:3258000/1‑69 (MQ=255)
                aCCGGGCTATGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTGCAata                                       >  1:109878/1‑69 (MQ=255)
                aCCGGGCTATGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTCCAata                                       >  1:2694790/1‑69 (MQ=255)
                        aTGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTGCAATATTTCGCCa                               <  1:1570357/69‑1 (MQ=255)
                        aTGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTGCAATATTTCGCCa                               <  1:622921/69‑1 (MQ=255)
                        aTGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTGCAATATTTCGCCa                               <  1:1203854/69‑1 (MQ=255)
                        aTGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTGCAATATTTCGCCa                               <  1:1322047/69‑1 (MQ=255)
                        aTGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTGCAATATTTCGCCa                               <  1:1315195/69‑1 (MQ=255)
                        aTGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTGCAATATTTCGCCa                               <  1:716973/69‑1 (MQ=255)
                                      atgGGCTTTAGCGCCTTCTGGGCAGGATTGGTTATCAg                                                <  1:1966216/38‑1 (MQ=255)
                                           cTTTAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCa            <  1:3258206/69‑1 (MQ=255)
                                           cTTTAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCa            <  1:653407/69‑1 (MQ=255)
                                            tttAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCa            <  1:852843/68‑1 (MQ=255)
                                                   cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGag    >  1:368657/3‑68 (MQ=255)
                                                   cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc    >  1:3046627/3‑69 (MQ=255)
                                                   cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc    >  1:613998/3‑69 (MQ=255)
                                                   cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc    >  1:3008495/3‑69 (MQ=255)
                                                   cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc    >  1:3024735/3‑69 (MQ=255)
                                                   cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc    >  1:2056545/3‑69 (MQ=255)
                                                   cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc    >  1:365555/3‑69 (MQ=255)
                                                   cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc    >  1:226824/3‑69 (MQ=255)
                                                   cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc    >  1:53072/3‑69 (MQ=255)
                                                   cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc    >  1:560571/3‑69 (MQ=255)
                                                   cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc    >  1:1728404/3‑69 (MQ=255)
                                                   cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc    >  1:809114/3‑69 (MQ=255)
                                                   cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc    >  1:1553847/3‑69 (MQ=255)
                                                   cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc    >  1:1505807/3‑69 (MQ=255)
                                                   cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc    >  1:1372916/3‑69 (MQ=255)
                                                   cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc    >  1:1207567/3‑69 (MQ=255)
                                                   cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc    >  1:117496/3‑69 (MQ=255)
                                                   cattCTGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc    >  1:577614/3‑69 (MQ=255)
                                                   cattCTCGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGAc    >  1:1932402/3‑69 (MQ=255)
                                                     cattGGGCAGGGTTGGTTATCAGCCTGCAATATTTTGCCACCTTGCTGAGCCGTCCTCATGCCGGACGt  >  1:2216959/4‑69 (MQ=255)
                                                                aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt              >  1:729976/1‑46 (MQ=255)
                                                                aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt              <  1:871368/46‑1 (MQ=255)
                                                                aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt              >  1:778474/1‑46 (MQ=255)
                                                                aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt              <  1:799211/46‑1 (MQ=255)
                                                                aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt              <  1:1014519/46‑1 (MQ=255)
                                                                aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt              <  1:407489/46‑1 (MQ=255)
                                                                aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt              >  1:3165208/1‑46 (MQ=255)
                                                                aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt              >  1:2724537/1‑46 (MQ=255)
                                                                aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt              >  1:2414441/1‑46 (MQ=255)
                                                                aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt              <  1:2313402/46‑1 (MQ=255)
                                                                aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt              <  1:2197001/46‑1 (MQ=255)
                                                                aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt              >  1:2080964/1‑46 (MQ=255)
                                                                aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt              >  1:1575281/1‑46 (MQ=255)
                                                                aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt              >  1:12463/1‑46 (MQ=255)
                                                                aTTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCt              >  1:1039054/1‑46 (MQ=255)
                                                                |                                                         
TGCCGCTCGCTGTATTACCGGGCTATGTCCATGATGTGATGGGCTTTAGCGCCTTCTGGGCAGGATTGGTTATCAGCCTGCAATATTTCGCCACCTTGCTGAGCCGCCCTCATGCCGGACGT  >  minE/2615559‑2615680

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